Project #2 -- Sequence Alignment

• Goal
• Be familiar with the techniques of sequence alighment
• Let you think the problem and solution thoroughly
• Project Description & Requirements
1. Please write the following sequence alignment programs.
2. Input data: two DNA sequences (each length = 1024), Scoring matrix={match s1, mismatch s2, indel s3}, no gap penalty.
1. Global alignment (ch6.6) (Scoring variable s1=+2,s2=-2,s3=-1)
2. Local alignment (ch6.8) (Scoring variable s1=+2,s2=-2,s3=-1)
3. Linear space alignment (ch7.2) (Scoring variable s1=+2,s2=0,s3=0)
4. Block alignment with Four-Russians speedup (ch7.3) (parameter t is dependent on your choice.) (Scoring variable s1=+2,s2=-2,s3=-1)
3. For each alignment argorithm, we your program should generate the following results:
   • your best alignment scores
   • show the best alignment segment with length 50
4. You need to write a report, including the following items:
   • Compare the time / space usage for alignment program 1 and 3
• Due

All stuff of this project, (runnable programs, packed source code files and your report) must send to TA before 6/5 5PM.